Cratons represent the oldest preserved lithospheric domains. Their lithosphere (lithospheric mantle welded to overlying Precambrian crystalline basement) is considered to be particularly robust and long-lived due to the protecting presence of buoyant and rigid “keels” made up of residual harzburgites. Although the cratons are mostly assumed to form in the Archaean, the timing of their formation remains poorly constrained. In particular, there are very few datasets describing concurrently the age of both the crustal and mantle portions of the lithosphere. In this study, we report new U–Pb ages and Hf isotope compositions for zircons in crustal xenoliths from the Udachnaya kimberlite in the central Siberian craton; this dataset includes samples from both the upper and lower portions of the crust. The zircon ages agree well with model melt-extraction Re–Os ages on refractory peridotite xenoliths from the same pipe; taken together they allow an integrated view of lithosphere formation. Our data reveal that the present day upper crust is Archaean, whereas both the lower crust and the lithospheric mantle yield Paleoproterozoic ages. We infer that the deep lithosphere beneath the Siberian craton was not formed in a single Archaean event, but grew in at least two distinct events, one in the late Archaean and the other in the Paleoproterozoic. Importantly, a complete or large-scale delamination and rejuvenation of the Archaean lower lithosphere (lower crust and lithospheric mantle) took place in the Paleoproterozoic. This further demonstrates that craton formation can be a protracted, multi-stage process, and that the present day crust and mantle may not represent complementary reservoirs formed through the same tectono-magmatic event. Further, deep cratonic lithosphere may be less robust and long living than often assumed, with rejuvenation and replacement events throughout its history.